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from glob import glob
import os
import sys
from setuptools import setup, Extension
from distutils.version import LooseVersion
from distutils.command.sdist import sdist as _sdist
from distutils.command.build_ext import build_ext as _build_ext
import versioneer
MIN_CYTHON_VERSION = '0.17'
if sys.version_info < (3, 4):
sys.stdout.write("At least Python 3.4 is required.\n")
sys.exit(1)
def no_cythonize(extensions, **_ignore):
"""
Change file extensions from .pyx to .c or .cpp.
Copied from Cython documentation
"""
for extension in extensions:
sources = []
for sfile in extension.sources:
path, ext = os.path.splitext(sfile)
if ext in ('.pyx', '.py'):
if extension.language == 'c++':
ext = '.cpp'
else:
ext = '.c'
sfile = path + ext
sources.append(sfile)
extension.sources[:] = sources
def check_cython_version():
"""exit if Cython not found or out of date"""
try:
from Cython import __version__ as cyversion
except ImportError:
sys.stdout.write(
"ERROR: Cython is not installed. Install at least Cython version " +
str(MIN_CYTHON_VERSION) + " to continue.\n")
sys.exit(1)
if LooseVersion(cyversion) < LooseVersion(MIN_CYTHON_VERSION):
sys.stdout.write(
"ERROR: Your Cython is at version '" + str(cyversion) +
"', but at least version " + str(MIN_CYTHON_VERSION) + " is required.\n")
sys.exit(1)
cmdclass = versioneer.get_cmdclass()
versioneer_build_ext = cmdclass.get('build_ext', _build_ext)
versioneer_sdist = cmdclass.get('sdist', _sdist)
class build_ext(versioneer_build_ext):
def run(self):
# If we encounter a PKG-INFO file, then this is likely a .tar.gz/.zip
# file retrieved from PyPI that already includes the pre-cythonized
# extension modules, and then we do not need to run cythonize().
if os.path.exists('PKG-INFO'):
no_cythonize(extensions)
else:
# Otherwise, this is a 'developer copy' of the code, and then the
# only sensible thing is to require Cython to be installed.
check_cython_version()
from Cython.Build import cythonize
self.extensions = cythonize(self.extensions)
versioneer_build_ext.run(self)
class sdist(versioneer_sdist):
def run(self):
# Make sure the compiled Cython files in the distribution are up-to-date
from Cython.Build import cythonize
check_cython_version()
cythonize(extensions)
versioneer_sdist.run(self)
cmdclass['build_ext'] = build_ext
cmdclass['sdist'] = sdist
extensions = [
Extension('sqt._helpers', sources=['sqt/_helpers.pyx']),
]
setup(
name = 'sqt',
version = versioneer.get_version(),
author = 'Marcel Martin',
author_email = 'marcel.martin@scilifelab.se',
url = 'https://bitbucket.org/marcelm/sqt',
description = 'Command-line tools for the analysis of high-throughput sequencing data',
license = 'MIT',
cmdclass = cmdclass,
packages = [ 'sqt', 'sqt.io', 'sqt.commands' ],
entry_points = {'console_scripts': [
'sqt = sqt.__main__:main',
#'sqt-addadapt = sqt.commands.addadapt:main',
#'sqt-bam2fastq = sqt.commands.bam2fastq:main',
#'sqt-bamstats = sqt.commands.bamstats:main',
#'sqt-checkfastqpe = sqt.commands.checkfastqpe:main',
#'sqt-checkvcfref = sqt.commands.checkvcfref:main',
#'sqt-compare-sequences = sqt.commands.compare_sequences:main',
#'sqt-coverage = sqt.commands.coverage:main',
#'sqt-fastaextract = sqt.commands.fastaextract:main',
#'sqt-fastamutate = sqt.commands.fastamutate:main',
#'sqt-fastastats = sqt.commands.fastastats:main',
#'sqt-fastxmod = sqt.commands.fastxmod:main',
#'sqt-fixbam64 = sqt.commands.fixbam64:main',
#'sqt-globalalign = sqt.commands.globalalign:main',
#'sqt-histogram = sqt.commands.histogram:main',
#'sqt-qualityguess = sqt.commands.qualityguess:main',
#'sqt-readcov = sqt.commands.readcov:main',
#'sqt-samfixn = sqt.commands.samfixn:main',
#'sqt-simreads = sqt.commands.simreads:main',
#'sqt-translate = sqt.commands.translate:main',
]},
install_requires = [
'pysam!=0.9.0',
'cutadapt',
'matplotlib',
'seaborn',
'xopen',
],
ext_modules = extensions,
test_suite = 'pytest',
classifiers = [
"Development Status :: 4 - Beta",
#Development Status :: 5 - Production/Stable
"Environment :: Console",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
)
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